A review of the recent advances on Lassa fever with special reference to molecular epidemiology and progress in vaccine development

Lassa fever, a viral hemorrhagic fever caused by the Lassa virus (LASV), is endemic in West Africa and is associated with high morbidity and mortality. At least three of the four proposed seven lineages of LASV are found in Nigeria, where the multimammate rat, Mastomys natalensis, serves as the primary reservoir. Endemic countries report approximately 200,000 infections and 5,000 deaths annually, with Nigeria experiencing thousands of infections and hundreds of deaths including healthcare workers. The aim of this review is to provide scientific information for better understanding of the evolutionary biology, molecular epidemiology, pathogenesis, diagnosis, and prevention of Lassa fever in Nigeria and other endemic regions worldwide, which can lead to improved control efforts and reduce morbidity and mortality from recurrent epidemics. To achieve this aim, observational studies such as case series, cross-sectional and cohort studies published between December 2017 and September 2022 were searched for on various online databases including Google Scholar, Africa Journals Online (AJOL), Research Gates, PubMed, PMIC, NCDC, and WHO websites. Although the origin and evolutionary history, and the transmission dynamics of Lassa virus have been revealed through recent. molecular epidemiological studies, the factors that drive the evolution of the virus remain unclear. Genetic changes in the viral genome may have enabled the virus to adapt to humans. Diagnosis of Lassa fever has also advanced from basic serological tests to more sophisticated methods such as quantitative real time polymerase chain reaction (qRT-PCR) and sequencing, which are particularly useful for identifying outbreak strains. Several vaccines, including recombinant vesicular stomatitis virus (rVSV), virus-like particle (VLP), and DNA-based vaccines, have shown promise in animal models and some have progressed to phase 2 clinical trials. Preventing and controlling Lassa fever is critical to safeguard the health and well-being of affected communities. Effective measures such as rodent control, improved sanitation, and early detection and isolation of infected individuals are essential for reducing transmission. Ongoing research into the genetic and ecological factors that drive the evolution of Lassa virus is necessary to reduce the impacts of Lassa fever.

A review of the recent advances on Lassa fever with special reference to molecular epidemiology and progress in vaccine development

Lassa fever, a viral hemorrhagic fever caused by the Lassa virus (LASV), is endemic in West Africa and is associated with high morbidity and mortality. At least three of the four proposed seven lineages of LASV are found in Nigeria, where the multimammate rat, Mastomys natalensis, serves as the primary reservoir. Endemic countries report approximately 200,000 infections and 5,000 deaths annually, with Nigeria experiencing thousands of infections and hundreds of deaths including healthcare workers. The aim of this review is to provide scientific information for better understanding of the evolutionary biology, molecular epidemiology, pathogenesis, diagnosis, and prevention of Lassa fever in Nigeria and other endemic regions worldwide, which can lead to improved control efforts and reduce morbidity and mortality from recurrent epidemics. To achieve this aim, observational studies such as case series, cross-sectional and cohort studies published between December 2017 and September 2022 were searched for on various online databases including Google Scholar, Africa Journals Online (AJOL), Research Gates, PubMed, PMIC, NCDC, and WHO websites. Although the origin and evolutionary history, and the transmission dynamics of Lassa virus have been revealed through recent molecular epidemiological studies, the factors that drive the evolution of the virus remain unclear. Genetic changes in the viral genome may have enabled the virus to adapt to humans. Diagnosis of Lassa fever has also advanced from basic serological tests to more sophisticated methods such as quantitative real time polymerase chain reaction (qRT-PCR) and sequencing, which are particularly useful for identifying outbreak strains. Several vaccines, including recombinant vesicular stomatitis virus (rVSV), virus-like particle (VLP), and DNA-based vaccines, have shown promise in animal models and some have progressed to phase 2 clinical trials. Preventing and controlling Lassa fever is critical to safeguard the health and well-being of affected communities. Effective measures such as rodent control, improved sanitation, and early detection and isolation of infected individuals are essential for reducing transmission. Ongoing research into the genetic and ecological factors that drive the evolution of Lassa virus is necessary to reduce the impacts of Lassa fever

La fièvre de Lassa, une fièvre hémorragique virale causée par le virus de Lassa (LASV), est endémique en Afrique de l'Ouest et est associée à une morbidité et une mortalité élevées. Au moins trois des quatre lignées proposées de LASV se trouvent au Nigeria, où le rat multimammaire, Mastomys natalensis, sert de réservoir principal. Les pays endémiques signalent environ 200,000 infections et 5,000 décès par an, le Nigéria connaissant des milliers d'infections et des centaines de décès, y compris des travailleurs de la santé. L'objectif de cette revue est de fournir des informations scientifiques pour une meilleure compréhension de la biologie évolutive, de l'épidémiologie moléculaire, de la pathogenèse, du diagnostic et de la prévention de la fièvre de Lassa au Nigeria et dans d'autres régions endémiques du monde, ce qui peut conduire à des efforts de contrôle améliorés et réduire la morbidité et la mortalité des épidémies récurrentes. Pour atteindre cet objectif, des études observationnelles telles que des séries de cas, des études transversales et de cohorte publiées entre décembre 2017 et septembre 2022 ont été recherchées sur diverses bases de données en ligne, notamment Google Scholar, Africa Journals Online (AJOL), Research Gate, PubMed, PMIC, Sites Web du NCDC et de l'OMS. Bien que l'origine et l'histoire évolutive, ainsi que la dynamique de transmission du virus de Lassa aient été révélées par des études épidémiologiques moléculaires récentes, les facteurs qui déterminent l'évolution du virus restent flous. Des modifications génétiques du génome viral pourraient avoir permis au virus de s'adapter à l'homme. Le diagnostic de la fièvre de Lassa est également passé des tests sérologiques de base à des méthodes plus sophistiquées telles que la réaction quantitative en chaîne par polymérase en temps réel (qRTPCR) et le séquençage, qui sont particulièrement utiles pour identifier les souches épidémiques. Plusieurs vaccins, y compris le virus recombinant de la stomatite vésiculeuse (rVSV), les particules pseudo-virales (VLP) et les vaccins à base d'ADN, se sont révélés prometteurs dans des modèles animaux et certains ont progressé vers des essais cliniques de phase 2. La prévention et le contrôle de la fièvre de Lassa sont essentiels pour préserver la santé et le bien-être des communautés touchées. Des mesures efficaces telles que le contrôle des rongeurs, l'amélioration de l'assainissement et la détection et l'isolement précoces des personnes infectées sont essentielles pour réduire la transmission. Des recherches continues sur les facteurs génétiques et écologiques qui déterminent l'évolution du virus de Lassa sont nécessaires pour réduire les impacts de la fièvre de Lassa.

A Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis / 生物医学与环境科学（英文）

OBJECTIVE@#A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis.@*METHODS@#In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 complete P. mirabilis genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation.@*RESULTS@#We identified a total of 205 CGs from 695 P. mirabilis strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( papC, papD, papE, papF, papG, papH, papI, papJ, and papK) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks.@*CONCLUSION@#This research innovatively performs high-resolution molecular typing of P. mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for P. mirabilis.

Profil épidémiologique des urgences chirurgicales viscérales pédiatriques au Centre Hospitalier Universitaire de Libreville / Epidemiological profile of pediatric visceral surgical emergencies at the Libreville University Hospital Center

Objectif : Etudier les urgences chirurgicales viscérales pédiatriques au Centre Hospitalier Universitaire de Libreville (CHUL).Patients et méthodes : Il s'agissait d'une étude prospective transversale monocentrique descriptive réalisée au CHUL du 1er janvier 2018 au 30 juin 2019. Les patients âgés de 0 à 15 ans ayant présenté une urgence chirurgicale viscérale dans les services des urgences, chirurgie viscérale et thoracique et de réanimation néonatale et néonatalogie ont été inclus.Résultats : Cette étude portait sur 156 patients. L'âge moyen était de 6,67 ans avec une prédominance du sexe masculin (107/49). Quarante-deux patients étaient référés d'autres structures sanitaires. La symptomatologie évoluait depuis plus de 3 jours chez 42,3% patients. Des explorations à visée diagnostique étaient réalisées dans 145 cas, dont 90 échographies, 51 radiographies de l'abdomen sans préparation et 4 TDM. Le délai de prise en charge était de plus de 6 heures dans 82,1% cas. La pathologie la plus rencontrée était l'appendicite aigue (53 cas). Nous avions répertorié 9 décès dont 7 en post-opératoire. La durée moyenne d'hospitalisation était de 7 jours avec des extrêmes de 3 et 54 jours.Conclusion : Les urgences chirurgicales viscérales occupent une place de choix dans la pathologie chirurgicale en général et chez l'enfant en particulier. La mortalité concerne majoritairement les nouveau-nés porteurs de malformations congénitales.

Objective: To study pediatric visceral surgical emergencies at the Center Hospitalier Universitaire de Libreville (CHUL).Patients and methods: This was a descriptive single-center cross-sectional prospective study carried out at the CHUL from January 1, 2018 to June 30, 2019. Patients aged 0 to 15 years having presented a visceral surgical emergency in the emergency departments, surgery visceral and thoracic and neonatal resuscitation and neonatology were included. Results: This study involved 156 patients. The average age is 6.67 years with a predominance of the male sex (107/49).Forty-two patients were referred from other health facilities. Symptoms have evolved for more than 3 days in 42.3% of patients. Diagnostic scans were performed in 145 cases, including 90 ultrasounds and 51 unprepared abdominal xrays and 4 CT scans. The time to treatment was more than 6 hours in 82.1% of cases. The most common pathology was acute appendicitis (53 cases). We have identified 9 deaths, including 7 postoperative. The average length of hospital stay was 7 days with extremes of 3 and 54 days. Conclusion: Visceral surgical emergencies occupy a prominent place in surgical pathology in general and in children in particular. Mortality mainly concerns newborns with congenital malformations.

Profil Épidémiologique et Mycologique de l'Otomycose à l'Hôpital Général de Référence de Niamey (Niger) / Epidemiological and my cologica l profile of otomycosisat the Genera l Reference Hospital o f Niamey (Niger

But. Décrire les caractéristiques épidémiologiques et mycologiques de l'otomycose à Niamey. Méthodologie.Il s'est agi d'une étude rétrospective menée sur 3ans au service d'ORL et CCF de l'Hôpital Général de Référence, portant sur les patients chez qui le diagnostic d'otomycose a été posé. Les paramètres étudiés étaient épidémiologiques et mycologiques. Résultats. En 3 ans, nous avons enregistré 447 consultations pour otites dont 56 avaient une otomycose, soit une fréquence de 12,53% de l'ensemble des otites et 58,92% des otites externes. L'âgemoyen était de 35,75 ans (extrêmes de 2 et 70 ans). La tranche d'âge de 31 à 60 ans représentait 58,93% des patients. Nous avons retrouvéune prédominance féminine (67,85%), (p=0,0752). Les principaux facteurs favorisant l'otomycose étaient le nettoyage de l'oreille au coton tige ou à la plume de volaille : (53,57%),le port du turban ou de couvre-chef, (46,42%), la baignade (16.07%), l'étroitesse du conduit auditif externe (8,92%) et le port de prothèse auditive externe intra-conduit (5,35%,). Sur le plan mycologique, le Candida albicanset l'Aspergilus nigeront représenté respectivement 19,44% et 33,33% des espèces fongiques isolées en culture. Conclusion. L'otomycose est une infection fréquente en Orl à Niamey. Le nettoyage de l'oreille au coton tige ou à la plume de volaille venait au premier rang des facteurs favorisant l'otite fongique. L'Aspergilus nigeret le Candida albicansétaient les germes les plus fréquemment isolés.

Estructura genética de cepas de Mycobacterium tuberculosis farmacorresistentes en Perú con base en haplotipos obtenidos de un ensayo de sonda lineal / Genetic structure of drug-resistant strains of Mycobacterium tuberculosis in Peru based on haplotypes obtained from a linear probe assay

RESUMEN Objetivo. Determinar la estructura genética de las cepas drogorresistentes de Mycobacterium tuberculosis que circularon en todo el Perú durante los años 2011-2015 a través de haplotipos obtenidos de un ensayo con sondas en línea. Materiales y métodos. Se analizaron 6589 muestras que ingresaron al Instituto Nacional de Salud para el diagnóstico rutinario mediante el ensayo GenoType® MTBDRplus v2, durante el periodo de estudio. Se crearon haplotipos resistentes mediante la concatenación de 21 sitios polimórficos de los genes evaluados por el ensayo con sondas en línea, y se realizó el análisis de asociación con fenotipos obtenidos por el método de proporciones agar 7H10. Resultados. Las mutaciones de mayores frecuencias fueron: rpoB S531L (55,4%) y rpoB D516V (18,5%) para la resistencia a rifampicina, y katG S315T (59,5%) e inhA c-15t (25,7%) para la resistencia a isoniacida. Se obtuvieron 13 haplotipos representativos (87,8% de muestras analizadas) de los cuales seis correspondieron al genotipo multidrogorresistente, cuatro al genotipo monorresistente a isoniacida y tres al genotipo monorresistente a rifampicina. Dieciocho departamentos, y la provincia del Callao, presentaron una alta diversidad haplotípica; cuatro presentaron moderada diversidad y dos presentaron baja diversidad. Conclusiones. Existe una alta diversidad haplotípica en la mayoría de los departamentos, además de una concentración de las cepas de Mycobacterium tuberculosis drogorresistentes en las ciudades de Lima y Callao. Asimismo, las cepas de Mycobacterium tuberculosis con perfil drogorresistente que circulan en el Perú contienen principalmente los marcadores genéticos de mayor prevalencia a nivel mundial asociados con la resistencia frente a rifampicina e isoniacida.

ABSTRACT Objective. To determine the genetic structure of drug-resistant strains of Mycobacterium tuberculosis that circulated throughout Peru during the years 2011-2015, by using haplotypes obtained from a line probe assay. Materials and methods. A total of 6589 samples that were admitted to the Instituto Nacional de Salud for routine diagnosis using the GenoType® MTBDRplus v2 assay were analyzed during the study period. Resistant haplotypes were created by concatenating 21 polymorphic sites of the evaluated genes using the line probe assay; and the association analysis was carried out with phenotypes obtained by the 7H10 agar ratio method. Results. The most frequent mutations were: rpoB S531L (55.4%) and rpoB D516V (18.5%) for rifampicin resistance, and katG S315T (59.5%) and inhA c-15t (25.7%) for isoniazid resistance. We obtained 13 representative haplotypes (87.8% of analyzed samples), 6 corresponded to the multidrug-resistant genotype, 4 to the isoniazid mono-resistant genotype and 3 to the rifampicin mono-resistant genotype. Eighteen regions and the province of Callao showed high haplotype diversity; four showed moderate diversity and two showed low diversity. Conclusions. Most regions showed high haplotype diversity; in addition, most drug-resistant strains of Mycobacterium tuberculosis were concentrated in the cities of Lima and Callao. Likewise, drug-resistant Mycobacterium tuberculosis strains circulating in Peru mainly contain the genetic markers with the highest prevalence worldwide, which are associated with resistance to rifampicin and isoniazid.

Caracterización de Escherichia coli D7111 productora de ß-LACTAMASA TEM-176 / Characterization of Escherichia coli D7111 producing the ß-LACTAMASA TEM-176

RESUMEN El presente reporte es la descripción original de bla TEM-176. Se caracterizaron los mecanismos de resistencia a antimicrobianos de un aislamiento de Escherichia coli enterotoxigénica, determinándose la resistencia a 22 antimicrobianos categorizados en 15 grupos diferentes mediante difusión en agar, estableciéndose grupo filogenético, mecanismos de resistencia y presencia de integrones de Clase 1 y 2 mediante PCR. Integrones y genes de resistencia a β-lactámicos fueron secuenciados. El aislamiento del grupo filogenético A, mostró resistencia o sensibilidad disminuida a ampicilina, amoxicilina más ácido clavulánico, ácido nalidíxico, ciprofloxacino, estreptomicina, kanamicina, tetraciclina, trimetoprim, sulfisoxazol, cotrimoxazol, azitromicina y nitrofurantoina, detectándose la presencia de bla TEM, aadA1/2, aphA1, sul3, tet(A) y un integron de Clase 2 conteniendo un gen dfrA1. La resistencia a quinolonas se relacionó con la substitución Ser83Ala. La secuencia de TEM mostró la substitución Ala222Val, la cual a la fecha no había sido descrita, reportándose como una nueva β-lactamasa, con el nombre de bla TEM-176.

ABSTRACT The present report is the original description of bla TEM-176. The mechanisms of resistance to antimicrobial agents were determined in an enterotoxigenic Escherichia coli, determining the susceptibility to 22 antimicrobials classified in 15 different groups by agar diffusion and establishing the phylogenetic group, mechanisms of resistance and presence of Class 1 and 2 integrons. Integrons and β-lactam resistance genes were sequenced. The isolate, belonging to phylogenetic group A, showed the presence of resistance or diminished susceptibility to a ampicillin, amoxicillin plus clavulanic acid, nalidíxic acid, ciprofloxacin, streptomycin, kanamycin, tetracycline, trimethoprim, sulfisoxazole, cotrimoxazole, azithromycin and nitrofurantoin, carrying bla TEM, aadA1/2, aphA1, sul3, tet(A) and a Class 2 integron containing a dfrA1 gene. Quinolone resistance was related to the substitution Ser83Ala. The TEM sequencing showed the presence of the new substitution Ala222Val, which led to the description of the new β-lactamase bla TEM-176.

Caracterización de Escherichia coli D7111 productora de ß-LACTAMASA TEM-176 / Characterization of Escherichia coli D7111 producing the ß-LACTAMASE TEM-176

RESUMEN El presente reporte es la descripción original de bla TEM-176. Se caracterizaron los mecanismos de resistencia a antimicrobianos de un aislamiento de Escherichia coli enterotoxigénica, determinándose la resistencia a 22 antimicrobianos categorizados en 15 grupos diferentes mediante difusión en agar, estableciéndose grupo filogenético, mecanismos de resistencia y presencia de integrones de Clase 1 y 2 mediante PCR. Integrones y genes de resistencia a β-lactámicos fueron secuenciados. El aislamiento del grupo filogenético A, mostró resistencia o sensibilidad disminuida a ampicilina, amoxicilina más ácido clavulánico, ácido nalidíxico, ciprofloxacino, estreptomicina, kanamicina, tetraciclina, trimetoprim, sulfisoxazol, cotrimoxazol, azitromicina y nitrofurantoina, detectándose la presencia de bla TEM, aadA1/2, aphA1, sul3, tet(A) y un integron de Clase 2 conteniendo un gen dfrA1. La resistencia a quinolonas se relacionó con la substitución Ser83Ala. La secuencia de TEM mostró la substitución Ala222Val, la cual a la fecha no había sido descrita, reportándose como una nueva β-lactamasa, con el nombre de bla TEM-176.

ABSTRACT The present report is the original description of bla TEM-176. The mechanisms of resistance to antimicrobial agents were determined in an enterotoxigenic Escherichia coli, determining the susceptibility to 22 antimicrobials classified in 15 different groups by agar diffusion and establishing the phylogenetic group, mechanisms of resistance and presence of Class 1 and 2 integrons. Integrons and β-lactam resistance genes were sequenced. The isolate, belonging to phylogenetic group A, showed the presence of resistance or diminished susceptibility to a ampicillin, amoxicillin plus clavulanic acid, nalidíxic acid, ciprofloxacin, streptomycin, kanamycin, tetracycline, trimethoprim, sulfisoxazole, cotrimoxazole, azithromycin and nitrofurantoin, carrying bla TEM, aadA1/2, aphA1, sul3, tet(A) and a Class 2 integron containing a dfrA1 gene. Quinolone resistance was related to the substitution Ser83Ala. The TEM sequencing showed the presence of the new substitution Ala222Val, which led to the description of the new β-lactamase bla TEM-176.

Molecular epidemiology and drug resistance of Acinetobacter baumannii isolated from a regional hospital in the Brazilian Amazon region

Abstract INTRODUCTION: In this study, we report a clonal dissemination of carbapenem resistant Acinetobacter baumannii isolates due to the acquisition of blaOXA-23 in a regional hospital located in Brazilian Amazon Region. METHODS: The isolates were identified by MALDI-TOF and the carbapenemase-encoding genes were detected by multiplex-PCR. The genetic similarity was investigated by pulsed-field gel electrophoresis (PFGE). RESULTS: Only 10 (55.6%) isolates harbored the gene bla OXA-23. PFGE analysis revealed that these isolates belong to a single clone. CONCLUSIONS: This dissemination strategy indicates the need for surveillance, adoption of control procedures defined in guidelines, and the careful administration of antimicrobials should be reinforced.

Molecular epidemiology of Pseudomonas aeruginosa isolated from lower respiratory tract of ICU patients / Epidemiologia molecular de Pseudomonas aeruginosa isolada em pacientes com infecções do trato respiratório inferior admitidos em UTI

Lower respiratory tract infections (LRTIs) caused by Pseudomonas aeruginosa are the most common infection among hospitalized patients, associated with increased levels of morbidity, mortality and attributable health care costs. Increased resistant Pseudomonas worldwide has been quite meaningful to patients, especially in intensive care unit (ICUs). Different species of Pseudomonas exhibit different genetic profile and varied drug resistance. The present study determines the molecular epidemiology through DNA fingerprinting method and drug resistance of P. aeruginosa isolated from patients with LTRIs admitted in ICU. A total of 79 P. aeruginosa isolated from patients with LRTIs admitted in ICU were characterized by Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD) and Repetitive Extrapalindromic PCR (REP-PCR). Antibiotic resistance was determined by minimum inhibitory concentration (MIC) assay while MDR genes, viz, blaTEM, blaOXA, blaVIM, blaCTX-M-15 were detected by polymerase chain reaction (PCR). Of the 137 Pseudomonas sp isolated from ICU patients, 57.7% of the isolates were reported to be P. aeruginosa. The overall prevalence of P. aeruginosa among the all included patients was 34.5%. The RAPD analysis yielded 45 different patterns with 72 clusters with 57% to 100% similarity level. The RFLP analysis yielded 8 different patterns with 14 clusters with 76% to 100% similarity level. The REP PCR analysis yielded 37 different patterns with 65 clusters with 56% to 100% similarity level. There was no correlation among the different DNA patterns observed between the three different methods. Predominant of the isolates (46.8%) were resistant to amikacin. Of the 79 isolates, 60.8% were positive for blaTEM gene and 39.2% were positive for blaOXA gene. P. aeruginosa was predominantly isolated from patients with LRTIs admitted in ICU. The difference in the similarity level observed between the three DNA fingerprinting methods indicates that there is high inter-strain variability. The high genetic variability and resistance patterns indicates that we should continuously monitor the trend in the prevalence and antibiotic resistance of P. aeruginosa especially in patients with LRTIs admitted in ICU.

Infecções do trato respiratório inferior (ITRIs) são as infecções mais comuns entre pacientes internados em unidade de terapia intensiva (UTI). Pseudomonas aeruginosa é a causa mais comum de ITRIs e está associada ao aumento da mortalidade. Diferentes espécies de Pseudomonas exibem diferentes perfis genéticos e resistência variada as drogas. O presente estudo determina a epidemiologia molecular através do método de fingerprinting de DNA e resistência as drogas de P. aeruginosa isoladas de pacientes com LTRIs internados em UTI. Um total de 79 P. aeruginosa isoladas de pacientes com ITRIs internados em UTI foram caracterizados por Polimorfismo de Comprimento de Fragmentos de Restrição (RFLP), DNA Polimórfico Amplificado ao Acaso (RAPD) e PCR Extrapalindrômico Repetitivo (REP-PCR). A resistência aos antibióticos foram determinadas pelos ensaios de concentrações inibitória mínima (MIC), enquanto os genes MDR, blaTEM, blaOXA, blaVIM, blaCTX-M-15 foram detectados pela reação em cadeia da polimerase (PCR). Das 137 Pseudomonas sp isoladas de pacientes de UTI, 57,7% dos isolados foram relatados como P. aeruginosa. A prevalência geral de P. aeruginosa entre os pacientes incluídos foram de 34,5%. A análise RAPD renderam 45 padrões diferentes com 72 clusters com nível de similaridade de 57% a 100%. A análise RFLP renderam 8 padrões diferentes com 14 clusters com 76% a 100% de similaridade. A análise de PCR do REP produziram 37 padrões diferentes com 65 clusters com nível de similaridade de 56% a 100%. Não houveram correlações entre os diferentes padrões de DNA observados entre os três diferentes métodos. Predominantes dos isolados (46,8%) eram resistentes à amicacina. Dos 79 isolados, 60,8% foram positivos para o gene blaTEM e 39,2% foram positivos para o gene blaOXA. P. aeruginosa foi predominantemente isolado de pacientes com ITRIs internados em UTI. A diferença no nível de similaridade observado entre os três métodos de fingerprinting do DNA indica que há alta variabilidade inter-strain. A alta variabilidade genética e os padrões de resistência indicam que devemos monitorar continuamente a tendência na prevalência e resistência a antibióticos de P. aeruginosa, especialmente em pacientes com ITRIs internados em UTI.

Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era: a literature review

Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.

Perfil Anatomopatológico e Imuno-histoquímico de Gliomas de Pacientes da Região de Maringá-PR / Anatomopathological and Immunohistochemical Profile of Gliomas of Patients in the Region of Maringá-PR / Perfil Anatomopatológico e Inmunohistoquímico de Gliomas en Pacientes la Región de Maringá-PR

Introdução: Os gliomas representam 80% dos tumores do sistema nervoso central. A Organização Mundial da Saúde (OMS) adicionou, em 2016, critérios moleculares na classificação dos gliomas. A fisiopatologia e os fatores de risco desses tumores ainda não são totalmente conhecidos. Objetivo: Realizar uma análise retrospectiva dos laudos anatomopatológicos e imuno-histoquímicos de gliomas. Método: Estudo transversal, retrospectivo e descritivo, a partir de exames anatomopatológicos e imuno-histoquímicos realizados entre janeiro de 2014 e dezembro de 2018 em um laboratório de anatomia patológica na cidade de Maringá-PR. Dos 234 laudos relacionados com o termo glioma, 204 foram selecionados para este estudo. Resultados: Foram encontrados tumores astrocitários, ependimários e oligodendrogliais, sendo que os astrocitomas corresponderam à maioria (86,8% dos casos encontrados). A média de idade ao diagnóstico foi de 51,8 anos e houve maior prevalência desses tumores no sexo masculino. Também foram analisadas mutações detectáveis por imuno-histoquímica como p53 (mutada em 66,7% dos testados), isocitrato desidrogenase (IDH) (28,6% mutados), X-linked alpha-thalassemia mental retardation (ATRX) (21,0%) e marcadores diagnósticos como o epithelial membrane antigen (EMA) positivo em todos os ependimomas analisados. Conclusão: É inegável a necessidade de novas pesquisas sobre os gliomas tanto no campo epidemiológico, tendo em vista a nova classificação, quanto no escopo fisiopatológico e clínico, com o objetivo de melhorar o entendimento sobre a patologia e o tratamento dos pacientes

Introduction: Gliomas represent 80% of the central nervous system tumors. World Health Organization (WHO) has added, in 2016, molecular features to the classification of gliomas. The pathophysiology and risk factors of these tumors are not yet fully understood. Objective: Perform a retrospective analysis of immunohistochemical and anatomopathological reports of gliomas. Method: Cross-sectional, retrospective and descriptive study carried out from anatomopathological and immunohistochemical exams made between January 2014 and December 2018 in a pathological anatomy laboratory in the city of Maringá-PR. Of the 234 reports related to the term glioma, 204 were selected for this study. Results: Astrocytic, ependymal and oligodendroglial tumors were found, with astrocytomas accounting for the majority (86.8% of the cases found). Mean age at diagnosis was 51.8 years and the prevalence was higher in men. Furthermore, immunohistochemically detectable mutations were analyzed, such as p53 (mutated in 66.7% of those tested), isocitrate dehydrogenase (IDH) (28.6% mutated), X-linked alpha-thalassemia mental retardation (ATRX) (21.0%) and diagnostic markers such as positive epithelial membrane antigen (EMA) in all analyzed ependymomas. Conclusion: The necessity of further researches on gliomas is undeniable , both epidemiologically considering the new classification and within the clinical and pathophysiological scope in order to improve the understanding of the pathology and the treatment for the patients

Introducción: Los gliomas representan 80% de los tumores del sistema nervioso central. La Organización Mundial de la Salud (OMS) agregó, en 2016, criterios moleculares sobre como clasificar los gliomas. La fisiopatología y los factores de riesgo de estos tumores aún no se comprenden completamente. Objetivo: Realizar un análisis retrospectivo de informes inmunohistoquímicos y anatomopatológicos de gliomas. Método: Estudio transversal, retrospectivo y descriptivo con base em pruebas anatomopatológicas e inmunohistoquímicas realizadas entre enero de 2014 y diciembre de 2018 en un laboratorio de anatomía patológica de la ciudad de Maringá-PR. De los 234 informes relacionados con el término glioma, se seleccionaron 204 para este estudio. Resultados: Se encontraron tumores astrocíticos, ependimarios y oligodendrogliales, siendo los astrocitomas la mayoría (86,8% de los casos encontrados). La edad media al diagnóstico fue de 51,8 años y hubo una mayor prevalencia de estos tumores en el sexo masculino. También se analizaron mutaciones detectables inmunohistoquímicamente, como p53 (mutado en 66,7% de los analizados), isocitrato desidrogenase(IDH) (28,6% mutado), X-linked alpha-thalassemia mental retardation (ATRX) (21,0%) y marcadores de diagnóstico como epithelial membrane antigen (EMA) positivo en todos los ependimomas analizados. Conclusión: Es innegable la necesidad de profundizaren las investigaciones sobre los gliomas, tanto en el campo epidemiológico, ante la nueva clasificación, como en el ámbito fisiopatológico y clínico, con el objetivo de mejorar el conocimiento sobre la patología y el tratamiento de los pacientes

Utilidad de la citometría de flujo para la detección de Pseudomonas aeruginosa productoras de metalobetalactamasas / Utility of flow citometry for detecting metallo-beta-lactamase-producing Pseudomonas aeruginosa

RESUMEN Con el objetivo de determinar la utilidad de la citometría de flujo para la detección de Pseudomonas aeruginosa productoras de metalobetalactamasas (MBL), se estudiaron aislamientos de P. aeruginosa genotípicamente caracterizados del cepario del laboratorio de Epidemiología Molecular y Genética de la Universidad Nacional Mayor de San Marcos. Se analizaron 29 aislamientos (17 productoras de MBL y 12 no productoras de MBL) con el kit de viabilidad celular FACSCalibur (Becton Dickinson). Se utilizaron dos tratamientos, uno con meropenem y el otro con meropenem-EDTA. Usando la razón de aumento de fluorescencia en las células no vivas, se demostró una diferencia significativa entre las productoras de MBL y las no MBL, considerando como punto de corte una razón >1,6. Se determinó una sensibilidad de 94,1% y una especificidad del 100%. La citometría de flujo constituye una alternativa para la detección de P. aeruginosa productora de MBL.

ABSTRACT In order to determine the utility of flow cytometry for detecting metallo-beta-lactamase (MBL)-producing Pseudomonas aeruginosa, we used genotypically characterized P. aeruginosa isolates from the Molecular Epidemiology and Genetics Laboratory of the Universidad Nacional Mayor de San Marcos. A total of 29 isolates (17 MBL-producing and 12 non-MBL-producing) were analyzed with the FACSCalibur (Becton Dickinson) cell viability kit. Two treatments were used, one with meropenem and the other with meropenem-EDTA. A significant difference between MBL and non-MBL-producing P. aeruginosa was demonstrated using the fluorescence ratio in non-living cells, considering a cut-off point of >1.6. We determined a sensitivity of 94.1% and a specificity of 100%. Flow cytometry represents an alternative for the detection of MBL-producing P. aeruginosa.

Tipificación del cassette cromosómico estafilocócico de Staphylococcus aureus resistentes al meticilino en el estado de Aragua, Venezuela / Typification of the staphylococcal chromosome cassette of methicillin-resistant Staphylococcus aureus in the state of Aragua, Venezuela

RESUMEN Objetivos: Tipificar el casette SCCmec en cepas de Staphylococcus aureus resistentes a meticilino (SARM) en aislados clínicos de centros de salud del Estado Aragua-Venezuela y comparar la presencia de los genotipos SCCmec entre los centros de salud del estado y según el tipo de infección. Materiales y métodos: Durante enero y agosto de 2015 se estudiaron 81 cepas SARM de cuatro centros de salud del estado de Aragua en Venezuela. La resistencia al meticilino se midió con el método de Kirby-Bauer con discos de oxacilina (1 µgr) y cefoxitina (30 µgr). El gen mecA y el SCCmec se analizaron por la técnica de reacción en cadena de polimerasa múltiple. Resultados: 55 aislados (67,9%) amplificaron el gen mecA, y 24 cepas (43,6%) amplificaron el SCCmec. El SCCmec I fue el más frecuente, seguido de SCCmecIV y SCCmec III, representaron el 62,5%, 25% y 12,5%, respectivamente. El SCCmec I fue predominante en el centro de salud A (80%), mientras que el SCCmec IV se encontró en el centro de salud B (60%) y C (100%). En el centro de salud D, 50% resultó ser SCCmec I y 50% SCCmec IVd. Se encontró relación entre el SCCmec y el centro de salud con significancia estadística. En infecciones de piel y tejidos blandos y en las respiratorias predominó el SCCmec I con 63,2% y 50% respectivamente. Conclusiones: La frecuencia de SCCmec I y IV permitirá establecer nuevas medidas en el uso y control de la resistencia a los antibióticos.

ABSTRACT Objective: Typify the SCCmec cassette in methicillin-resistant strains of Staphylococcus aureus in clinical isolates from health centers in the State of Aragua-Venezuela and compare the presence of SCCmec genotypes among the state health centers and according to the type of infection. Materials and methods: 81 MRSA strains from four health centers of the Aragua-Venezuela State were studied. Methicillin resistance was performed with the Kirby-Bauer method with oxacillin (1 µg) and cefoxitin (30 µg) disks. The mecA gene and SCCmec were analyzed by the multiple PCR technique. Results: Only 55 isolates (67.9%) amplified the mecA gene, and 24 strains (43.6%) amplified SCCmec. SCCmec type I was the most frequency, followed by SCCmec IV and SCCmec III, representing 62.5%, 25% and 12.5%, respectively. SCCmec I was predominant in health center A (80%), while in B and C 60% and 100% respectively were SCCmec IV. At health center D, 50% turned out to be SCCmec I and 50% SCCmec IVd. A relationship was found between the SCCmec and the health center with statistical significance. SCCmec I predominated in skin and soft tissue and respiratory infections with 63.2% and 50%, respectively. There was no association between genotype and type of infection with a p value greater than 0.05. Conclusions: The prevalence of SCCmec I and IV will allow establishing new measures in the use of antibiotics and epidemiological control.

Medicina de precisión: aspectos prácticos para el cirujano moderno / Precision medicine: practical aspects for the modern surgeon

Los contenidos de este capítulo se basan en la 3a edición de las Clínicas Quirúrgicas de Cáncer Colorrectal. C. Vaccaro y N. Peralta. del hospital ediciones 2020 (en prensa)

Análise Epidemiológica e Molecular do vírus Hepatite A em Pacientes Atendidos entre 2013 a 2019 no Ambulatório de Hepatites Virais do Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro / Epidemiological and Molecular Analysis of the Hepatitis A Virus in Patients Attended Between 2013 and 2019 at the Viral Hepatitis Outpatient Clinic of the Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro

Ao longo dos anos vem se observando um declínio do número de casos de infecção pelo vírus da hepatite A (HAV) em crianças, relacionado ao investimento nos programas de vacinação e a melhorias sanitárias. Porém, nota se a mudança desse perfil de infecção, onde indivíduos jovens/adultos vêm sendo mais acometidos. Apesar do vírus ser transmitido principalmente pelo consumo de água e alimentos contaminados, diversos surtos têm ocorrido ao redor do mundo em adultos e sendo relacionados a práticas sexuais. Em nosso país, um aumento no número de casos nos últimos três anos foi observado após um período de declínio de notificações. Assim, este estudo teve como objetivo avaliar os comportamentos de risco e os aspectos moleculares associados à transmissão do HAV em indivíduos atendidos no Ambulatório de Hepatites Virais do Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, entre os anos de 2017 e 2019. Para tal, foram coletadas amostras de soro e informações socioepidemiológicas de 52 pacientes com anti-HAV IgM reagente, que chegaram ao ambulatório. Posteriormente, essas amostras tiveram o genoma viral extraído e analisado através da técnica de RTPCR. Após detecção, o RNA foi sequenciado e analisado filogeneticamente. Em seguida, foram realizadas análises filogeográficas para obter a rota de dispersão e período de introdução das estirpes virais no país. (AU)

Com a análise dos dados dos prontuários, observou-se que 78,9% (41/52) pacientes eram do sexo masculino, nas faixas etárias 20 a 29 anos (n=24/52) e de 30 a 39 anos (n=20/52) com media 32,1 anos, sendo 63,5% (n=33) dele(a)s homens/mulheres que fazem sexo com homens/mulheres (HSH/MSM), e 89,9% eram residentes na região norte da cidade do Rio de Janeiro. Observou-se uma baixa frequência de exposição a fatores hídricos, alimentares e parenterais na população estudada, sendo 42,3%, 42,3%, 34,7%, respectivamente. Já algumas práticas sexuais apresentaram elevada frequência, destacando o sexo oral (75%) e sexo anal (65,3%). Através das análises filogenéticas, foi identificado um único subgenótipo IA da população estudada. Quatro clados deste subgenótipo foram formados, dos quais, três agruparamse as sequências dos estirpes virais provenientes de surtos Europeus/Asiáticos, e um clado, formado por estirpes virais previamente circulantes no Brasil. Através da filogeografia, foi possível inferir o ano e país de introdução, além da data de origem das estirpes virais no Brasil. A estirpe VRD_521_2016 foi possivelmente introduzida entre 2016-2017 pela Espanha com provável origem em 2013, a RIVM-HAV16-090 europeia/asiática e V16-25801, possivelmente introduzida pela Alemanha, entre 20142015 e 2015-2016 respectivamente, com provável origem em 2000 e 2011. Nossos achados reforçam a necessidade de ampliação do acesso à vacina contra o HAV a grupos adultos de risco e do monitoramento da entrada de novos patógenos no Brasil. Além disso, medidas educativas são úteis para impedir a disseminação do HAV em populações-chave como os HSH. (AU)

Prevalence and molecular characterization of Cryptosporidium spp. in Père Davids deer (Elaphurus davidianus) in Jiangsu, China / Prevalência e caracterização molecular de Cryptosporidium spp. no cervo de Père David (Elaphurus davidianus) em Jiangsu, China

Abstract Cryptosporidium is a zoonotic parasite that causes diarrhea in a broad range of animals, including deer. Little is known about the prevalence and genotype of Cryptosporidium spp. in Père David's deer. In this study, 137 fecal samples from Père David's deer were collected between July 2017 and August 2018 in the Dafeng Reserve and analyzed for Cryptosporidium spp. by nested-PCR based on the small subunit ribosomal RNA (SSU rRNA) gene, followed by sequence analyses to determine the species. The 60 kDa glycoprotein (gp60) gene was used to characterize Cryptosporidium spp. Among 137 samples, 2 (1.46%) were positive for Cryptosporidium spp. according to SSU rRNA gene sequencing results. Both samples belonged to the Cryptosporidium deer genotype, with two nucleotide deletions and one nucleotide substitution. The prevalence data and molecular characterization of this study provide basic knowledge for controlling and preventing Cryptosporidium infections in Père David's deer in this area.

Resumo Cryptosporidium é um parasita zoonótico que causa diarreia em uma ampla gama de animais, incluindo veados. Pouco se sabe sobre a prevalência e o genótipo de Cryptosporidium spp. no cervo de Père David. Neste estudo, 137 amostras fecais do cervo de Père David foram coletadas entre julho de 2017 e agosto de 2018, na Reserva Dafeng, e analisadas para Cryptosporidium spp. por nested-PCR baseado no gene do RNA ribossômico da subunidade pequena (SSU rRNA), seguido de análises de sequências para determinar as espécies. O gene da glicoproteína de 60 kDa (gp60) foi utilizado para caracterizar Cryptosporidium spp. Dentre as 137 amostras, 2 (1,46%) foram positivas para Cryptosporidium spp. de acordo com os resultados do sequenciamento gênico de SSU rRNA. Ambas as amostras pertenciam ao genótipo do cervo Cryptosporidium, com duas deleções nucleotídicas e uma substituição nucleotídica. Os dados de prevalência e a caracterização molecular deste estudo fornecem conhecimentos básicos para controlar e prevenir infecções por Cryptosporidium nos cervos de Père David nessa.

RT-nPCR Assays for Amplification and Sequencing of VP1 Genes in Human Enterovirus A-D from Clinical Specimens / 生物医学与环境科学（英文）

Objective@#To develop RT-nPCR assays for amplifying partial and complete VP1 genes of human enteroviruses (HEVs) from clinical samples and to contribute to etiological surveillance of HEV-related diseases.@*Methods@#A panel of RT-nPCR assays, consisting of published combined primer pairs for VP1 genes of HEV A-C and in-house designed primers for HEV-D, was established in this study. The sensitivity of each RT-nPCR assay was evaluated with serially diluted virus stocks of five serotypes expressed as CCID @*Results@#The sensitivity of RT-nPCR assays for amplifying partial VP1 gene of HEVs was 0.1 CCID @*Conclusion@#This RT-nPCR system is capable of amplifying the partial and complete VP1 gene of HEV A-D, providing rapid, sensitive, and reliable options for molecular typing and molecular epidemiology of HEVs in clinical specimens.

Molecular epidemiology and characterization of Streptococcus mutans strains in Korea / 대한구강보건학회지

OBJECTIVES: We investigated the characteristics of Streptococcus mutans in the national culture collection from Korea. Twenty-nine (dental plaque, n=27; endodontic infections, n=1; blood, n=1) isolates were included in this study.METHODS: Antimicrobial susceptibilities were tested using the disk diffusion test. Multilocus sequence typing (MLST), serotyping, and collagen-binding genes were used for polymerase chain reaction (PCR) and direct sequencing. A collagen-binding (to assess the adhesion properties) assay was performed. S. mutans demonstrated high susceptibility to antimicrobial agents. Differences in collagen-binding abilities of the cnm-positive and -negative groups were compared using the Mann-Whitney U test (P<0.05).RESULTS: MLST analyses revealed 25 sequence types (STs), 17 of which (ST213-ST229) contained new alleles. The strains were classified into four serotypes with the c type encompassing 79.3% of all strains, while the e, f, and k types representing 6.9% each. Analysis of the cnm and cbm genes, which encode the two surface adhesin components of S. mutans, revealed three cnm-positive strains, each displaying greater adhesion ability than those of the cnm-negative strains.CONCLUSIONS: This study highlights the presence of a wide variety of S. mutans genotypes in Korea. These findings may provide useful information regarding the pathogenesis of infectious diseases, such as dental caries.